@article{walker_maynor_isik_heine_whetten_payn_quate_mckeand_2024, title={Stem Defect Rates and Ice Storm Damage for Families of Pinus taeda from Coastal and Piedmont Provenances Planted on a North Carolina Piedmont Site}, volume={4}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxae016}, DOI={10.1093/forsci/fxae016}, abstractNote={Abstract
               Twenty Pinus taeda L. families from both the Coastal Plain and Piedmont provenances in the southeastern United States were planted on an upper Piedmont site that experienced a severe ice storm at age 3 years. Storm damage and defect rates through age 11 years were compared with the seed transfer distance and the seed parents’ breeding values to develop prediction models for storm damage and rates of forking, stem break, and sawtimber potential. Warmer-source families had higher probability of limb or stem breaks and foliage injury from the storm. Taller trees were more likely to experience breaks and foliage injury, even after accounting for seed transfer distance. Trees with forks or fusiform rust (Cronartium quercuum f. sp. fusiforme) infection had a higher probability of breaks. Trees with limb breaks or foliage injury did not have reduced sawtimber potential, but broken stems reduced sawtimber potential. The storm did not cause immediate mortality, but trees with major limb breaks, stem breaks, or foliage injury were less likely to be alive at age 8 years. At age 11 years, families with the best combination of breeding values for forking, straightness, and rust resistance had a predicted 60% of stems having sawtimber potential, whereas families with the worst combination had 30%.
               Study Implications: Planting warmer-source Pinus taeda (loblolly pine) families farther north and inland may lead to greater growth but poses a risk of damage from cold temperatures and ice storms. Trees grown for solid-wood products must be relatively defect-free and require a longer rotation, whereas bioenergy and pulpwood can use smaller, defective trees. This analysis presents predictions of defect rates through age 11 years based on the seed source and breeding values using data from a planting in the upper Piedmont of North Carolina. Land managers can use these models to weigh the benefits and risks when choosing families for reforestation.}, journal={FOREST SCIENCE}, author={Walker, Trevor D. and Maynor, Jessica A. and Isik, Fikret and Heine, Austin J. and Whetten, Ross W. and Payn, Kitt G. and Quate, T. Austin and McKeand, Steven E.}, year={2024}, month={Apr} }
 @article{shalizi_walker_heine_payn_isik_bullock_mckeand_2023, title={Performance Based on Measurements from Individual-Tree Progeny Tests Strongly Predicts Early Stand Yield in Loblolly Pine}, volume={2}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxad002}, DOI={10.1093/forsci/fxad002}, abstractNote={Abstract
               To facilitate the utility of genetic improvement in loblolly pine, individual-tree volume (productivity) scores estimated from single-tree plot or row-plot progeny test designs were compared with stand-level volume per unit area from block plots. A large number of families representing a wide range of progeny test scores for volume were established in growth and yield trials to generalize the results to families created by the breeding program. Individual-tree volume scores from progeny tests strongly corresponded with stand-level volume from block plots, especially after accounting for site quality and the risk of fusiform rust disease. A ten-point increase in the volume score from progeny test data was estimated to increase stand-level volume by 3.9 m3 ha-1 at age 6 years. A prediction model is presented that includes a new statistic, rust risk index, which is the expected rust incidence for a family at a new site when the hazard of rust for a checklot can be estimated from historical data. The study results through age 6 years corroborate the Performance Rating System as effective in guiding family deployment decisions. The models presented are based on pre-crown closure data at 6 years and will be updated with older measurements as the study matures.
               Study Implications: The Performance Rating System (PRS™) has been a successful tool for presenting genetic merit of improved loblolly pine families for landowners and forest managers in a more coherent and standardized manner. This system can be easily applied in other forest tree improvement programs, because it makes genetic improvement user-friendly for silviculturists and forest managers. Landowners can use this system to make decisions for selecting improved families suited to their specific forest management objectives. Seed orchard and nursery managers also depend on the PRS to choose the families to produce and as a third-party verification to market their genetic merit to customers. This study demonstrates that higher stand-level volume per unit area can be achieved when forest managers plant fast growing families with low fusiform rust disease risk on productive sites. The combined effect of genetic improvement for productivity and fusiform rust disease resistance is significant on stand-level volume per unit area.}, journal={FOREST SCIENCE}, author={Shalizi, Mohammad Nasir and Walker, Trevor D. and Heine, Austin J. and Payn, Kitt G. and Isik, Fikret and Bullock, Bronson P. and McKeand, Steven E.}, year={2023}, month={Feb} }
 @article{shalizi_payn_walker_isik_heine_mckeand_2022, title={Long-term evaluation of intra- and inter-provenance hybrids of loblolly pine in the Piedmont region of the southeastern United States}, volume={522}, ISSN={["1872-7042"]}, url={http://dx.doi.org/10.1016/j.foreco.2022.120469}, DOI={10.1016/j.foreco.2022.120469}, abstractNote={Long-term response of two intra- and two inter-provenance populations of loblolly pine (Pinus taeda L.) were evaluated in the Piedmont region of the southeastern United States. In total, 82 polycross families of the Atlantic Coastal (C) and Piedmont (P) provenances (C×C, P×P) and their hybrids (C×P, P×C) were field tested for growth, sawtimber potential, and survival through age 19 years. The Coastal pure (C×C) families were the tallest, and the hybrid populations (C×P, P×C) were intermediate for height. The four populations did not differ for diameter at breast height. The hybrid C×P population, followed by the C×C population, showed significantly higher stand volumes per hectare. These two populations maintained higher survival and stand density compared to the Piedmont pure populations. Sawtimber potential was significantly higher in the Piedmont pure families at the coldest study sites, presumably due to defect in the C×C and C×P from cold damage. No significant genotype-by-environment interactions were detected for any traits. The genetic gain for height, stand volume, and survival was considerable in the C×C and C×P over the Piedmont source, suggesting potential for benefiting from the faster growth of the Coastal material in the Piedmont region. The performance of the Coastal intra- and inter-provenance populations was marginally affected by the minimum winter temperatures (MWT). These results indicate that the Coastal and the hybrid families can be planted in the Piedmont region with MWT’s of −13 °C or greater and where the difference in MWT between the origin of the Coastal parents and the test sites was not extreme (e.g., the difference did not exceed 2.8 °C). These MWT limits encompass the southern Piedmont of North Carolina (<35.615 °N) and the Piedmont of South Carolina, Georgia, and Alabama.}, journal={FOREST ECOLOGY AND MANAGEMENT}, publisher={Elsevier BV}, author={Shalizi, Mohammad Nasir and Payn, Kitt G. and Walker, Trevor D. and Isik, Fikret and Heine, Austin J. and McKeand, Steven E.}, year={2022}, month={Oct} }
 @article{heine_walker_jett_isik_mckeand_2022, title={Pollination Bag Type Affects Ovule Development and Seed Yields in Pinus taeda L.}, volume={12}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxac052}, DOI={10.1093/forsci/fxac052}, abstractNote={Abstract
               Loblolly pine (Pinus taeda L.) is the most widely planted forest tree species in the United States. Most of the seedlings used to establish these plantations come from seed collected in open-pollinated seed orchards, but an increasing number are coming from controlled crosses, about 15%–20% of the loblolly pine seedling crops in the last five years. To produce this seed, millions of pollination bags are installed each spring in orchards throughout the southeastern United States; over 2.6 million bags were installed in 2022. This study evaluated 13 pollination bag types available for use in the mass production of control-cross seed. Using cone analysis, significant differences were found among bag types for the proportion of ovules resulting in filled seed, empty seed, and first-year aborts. Due to differences in the efficacy of orchard management, study trees varied greatly in their proportion of ovules resulting in filled seed and first-year aborts. Under good orchard management, open-pollinated cones had 72% of their ovules as filled seed and 12% in first-year aborted ovules. The best pollination bag type had 62% of its ovules as filled seed with 22% in first-year aborted ovules. These differences are apparently due to the quality of pollen used in the controlled crosses.
               Study Implications: Compared with open-pollinated families, full-sibling crosses among elite parents of loblolly pine produce more market value to landowners due to greater productivity, increased disease resistance, and enhanced stem form. Specific crosses of loblolly pine have occupied about 15%–20% of the recent seedling market because the seed are costly and difficult to produce. This study tested pollination bag types to determine their effectiveness in producing control-cross seed. Some bag types were superior in increasing seed yield, but seed yields for open-pollinated cones tended to be higher, suggesting problems in the control-cross process. Cone analysis is a useful tool for seed orchard managers to diagnose problems in seed production. Understanding and correcting these problems will help managers increase their production of full-sibling seed and lead to the establishment of new plantations with increased forest productivity.}, journal={FOREST SCIENCE}, author={Heine, Austin J. and Walker, Trevor D. and Jett, Jackson B. and Isik, Fikret and McKeand, Steven E.}, year={2022}, month={Dec} }
 @article{lu_payn_pandey_acosta_heine_walker_young_2021, title={HYPERSPECTRAL IMAGING WITH COST-SENSITIVE LEARNING FOR HIGH-THROUGHPUT SCREENING OF LOBLOLLY PINE (PINUS TAEDA L.) SEEDLINGS FOR FREEZE TOLERANCE}, volume={64}, ISSN={["2151-0040"]}, url={http://dx.doi.org/10.13031/trans.14708}, DOI={10.13031/trans.14708}, abstractNote={HighlightsA hyperspectral imaging approach was developed for freeze-tolerance phenotyping of loblolly pine seedlings.Image acquisition was conducted before and periodically after artificial freezing of the seedlings.A hyperspectral data processing pipeline was developed to extract the spectra from seedling segments.Cost-sensitive support vector machine (SVM) was used for classifying stressed and healthy seedlings.Post-freeze scanning of seedlings on day 41 achieved the highest screening accuracy of 97%.Abstract. Loblolly pine (Pinus taeda L.) is a commercially important timber species planted across a wide temperature gradient in the southeastern U.S. It is critical to ensure that the planting stock is suitably adapted to the growing environment to achieve high productivity and survival. Long-term field studies, although considered the most reliable method for assessing cold hardiness of loblolly pine, are extremely resource-intensive and time-consuming. The development of a high-throughput screening tool to characterize and classify freeze tolerance among different genetic entries of seedlings will facilitate accurate deployment of highly productive and well-adapted families across the landscape. This study presents a novel approach using hyperspectral imaging to screen loblolly pine seedlings for freeze tolerance. A diverse population of 1549 seedlings raised in a nursery were subjected to an artificial mid-winter freeze using a freeze chamber. A custom-assembled hyperspectral imaging system was used for in-situ scanning of the seedlings before and periodically after the freeze event, followed by visual scoring of the frozen seedlings. A hyperspectral data processing pipeline was developed to segment individual seedlings and extract the spectral data. Examination of the spectral features of the seedlings revealed reductions in chlorophylls and water concentrations in the freeze-susceptible plants. Because the majority of seedlings were freeze-stressed, leading to severe class imbalance in the hyperspectral data, a cost-sensitive learning technique that aims to optimize a class-specific cost matrix in classification schemes was proposed for modeling the imbalanced hyperspectral data, classifying the seedlings into healthy and freeze-stressed phenotypes. Cost optimization was effective for boosting the classification accuracy compared to regular modeling that assigns equal costs to individual classes. Full-spectrum, cost-optimized support vector machine (SVM) models achieved geometric classification accuracies of 75% to 78% before and within 10 days after the freeze event, and up to 96% for seedlings 41 days after the freeze event. The top portions of seedlings were more indicative of freeze events than the middle and bottom portions, leading to better classification accuracies. Further, variable selection enabled significant reductions in wavelengths while achieving even better accuracies of up to 97% than full-spectrum SVM modeling. This study demonstrates that hyperspectral imaging can provide tree breeders with a valuable tool for improved efficiency and objectivity in the characterization and screening of freeze tolerance for loblolly pine. Keywords: Cost-sensitive learning, Freeze tolerance, Hyperspectral imaging, Plant phenotyping, Support vector machine.}, number={6}, journal={TRANSACTIONS OF THE ASABE}, publisher={American Society of Agricultural and Biological Engineers (ASABE)}, author={Lu, Yuzhen and Payn, Kitt G. and Pandey, Piyush and Acosta, Juan J. and Heine, Austin J. and Walker, Trevor D. and Young, Sierra}, year={2021}, pages={2045–2059} }
 @article{pandey_payn_lu_heine_walker_acosta_young_2021, title={Hyperspectral Imaging Combined with Machine Learning for the Detection of Fusiform Rust Disease Incidence in Loblolly Pine Seedlings}, volume={13}, ISSN={["2072-4292"]}, url={https://doi.org/10.3390/rs13183595}, DOI={10.3390/rs13183595}, abstractNote={Loblolly pine is an economically important timber species in the United States, with almost 1 billion seedlings produced annually. The most significant disease affecting this species is fusiform rust, caused by Cronartium quercuum f. sp. fusiforme. Testing for disease resistance in the greenhouse involves artificial inoculation of seedlings followed by visual inspection for disease incidence. An automated, high-throughput phenotyping method could improve both the efficiency and accuracy of the disease screening process. This study investigates the use of hyperspectral imaging for the detection of diseased seedlings. A nursery trial comprising families with known in-field rust resistance data was conducted, and the seedlings were artificially inoculated with fungal spores. Hyperspectral images in the visible and near-infrared region (400–1000 nm) were collected six months after inoculation. The disease incidence was scored with traditional methods based on the presence or absence of visible stem galls. The seedlings were segmented from the background by thresholding normalized difference vegetation index (NDVI) images, and the delineation of individual seedlings was achieved through object detection using the Faster RCNN model. Plant parts were subsequently segmented using the DeepLabv3+ model. The trained DeepLabv3+ model for semantic segmentation achieved a pixel accuracy of 0.76 and a mean Intersection over Union (mIoU) of 0.62. Crown pixels were segmented using geometric features. Support vector machine discrimination models were built for classifying the plants into diseased and non-diseased classes based on spectral data, and balanced accuracy values were calculated for the comparison of model performance. Averaged spectra from the whole plant (balanced accuracy = 61%), the crown (61%), the top half of the stem (77%), and the bottom half of the stem (62%) were used. A classification model built using the spectral data from the top half of the stem was found to be the most accurate, and resulted in an area under the receiver operating characteristic curve (AUC) of 0.83.}, number={18}, journal={REMOTE SENSING}, publisher={MDPI AG}, author={Pandey, Piyush and Payn, Kitt G. and Lu, Yuzhen and Heine, Austin J. and Walker, Trevor D. and Acosta, Juan J. and Young, Sierra}, year={2021}, month={Sep} }
 @article{lu_walker_acosta_young_pandey_heine_payn_2021, title={Prediction of Freeze Damage and Minimum Winter Temperature of the Seed Source of Loblolly Pine Seedlings Using Hyperspectral Imaging}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxab003}, DOI={10.1093/forsci/fxab003}, abstractNote={Abstract
               The most important climatic variable influencing growth and survival of loblolly pine is the yearly average minimum winter temperature (MWT) at the seed source origin, and it is used to guide the transfer of improved seed lots throughout the species’ distribution. This study presents a novel approach for the assessment of freeze-induced damage and prediction of MWT at seed source origin of loblolly pine seedlings using hyperspectral imaging. A population comprising 98 seed lots representing a wide range of MWT at seed source origin was subjected to an artificial freeze event. The visual assessment of freeze damage and MWT were evaluated at the family level and modeled with hyperspectral image data combined with chemometric techniques. Hyperspectral scanning of the seedlings was conducted prior to the freeze event and on four occasions periodically after the freeze. A significant relationship (R2 = 0.33; p < .001) between freeze damage and MWT was observed. Prediction accuracies of freeze damage and MWT based on hyperspectral data varied among seedling portions (full-length, top, middle, and bottom portion of aboveground material) and scanning dates. Models based on the top portion were the most predictive of both freeze damage and MWT. The highest prediction accuracy of MWT [RPD (ratio of prediction to deviation) = 2.12, R2 = 0.78] was achieved using hyperspectral data obtained prior to the freeze event. Adoption of this assessment method would greatly facilitate the characterization and deployment of well-adapted loblolly pine families across the landscape.}, number={3}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Lu, Yuzhen and Walker, Trevor D. and Acosta, Juan J. and Young, Sierra and Pandey, Piyush and Heine, Austin J. and Payn, Kitt G.}, year={2021}, month={Jun}, pages={321–334} }
 @article{maynor_isik_walker_whetten_heine_payn_mckeand_2021, title={Provenance and Family Variation in Biomass Potential of Loblolly Pine in the Piedmont of North Carolina}, volume={67}, ISSN={["1938-3738"]}, url={https://doi.org/10.1093/forsci/fxaa056}, DOI={10.1093/forsci/fxaa056}, abstractNote={Abstract
               Considerable genetic differences in loblolly pine (Pinus taeda L.) exist for growth, stem form, and wood quality traits that influence biomass/biofuel production. By planting genetically superior trees with desirable biomass/biofuel traits, it is possible to substantially increase the amount of biomass and potential sawtimber trees produced from plantations. Ten of the fastest growing loblolly pine families from two provenances, Atlantic Coastal Plain and Piedmont, were tested for their biomass potential in North Carolina on a Piedmont site. At this northern Piedmont site at age six years, there were no provenance differences for biomass production or for trees with sawtimber potential. Variation in volume and sawtimber potential was significant at the family level. For biomass plantations, risks can be mitigated because of shorter rotation length, allowing for a higher-risk seed lot to capture greater gains in terms of volume. For a longer-rotation sawtimber stand, a more conservative family deployment strategy should be considered to maintain stem quality at the end of the rotation. Understanding the different seed source families and harvest regimes is essential to ensure profitable returns from pine plantations.}, number={3}, journal={FOREST SCIENCE}, publisher={Oxford University Press (OUP)}, author={Maynor, Jessica A. and Isik, Fikret and Walker, Trevor D. and Whetten, Ross W. and Heine, Austin J. and Payn, Kitt G. and McKeand, Steven E.}, year={2021}, month={Jun}, pages={312–320} }
 @article{mckeand_payn_heine_abt_2020, title={Economic Significance of Continued Improvement of Loblolly Pine Genetics and Its Efficient Deployment to Landowners in the Southern United States}, volume={119}, ISSN={0022-1201 1938-3746}, url={http://dx.doi.org/10.1093/jofore/fvaa044}, DOI={10.1093/jofore/fvaa044}, abstractNote={AbstractThe economic consequence of continuing or increasing the tree improvement efforts for loblolly pine (Pinus taeda L.) in the southern United States is immense. For the more than one million acres planted each year with germplasm from the North Carolina State University Cooperative Tree Improvement Program, the present value of continuing current tree breeding efforts and deploying the genetic gains to landowners is estimated to be more than $1.7 billion at current prices. The present value of increasing the rate of genetic gain from 1% per year to 1.1% per year is $211 million. These analyses can be used to justify maintaining and even increasing efforts in tree improvement. With the aggressive fourth-cycle breeding program underway and plans for fifth-cycle breeding and deployment strategies being developed, we have every reason to believe that this trend for at least 1% gain per year will continue for decades, provided the resources to continue tree improvement efforts remain available. Even a modest increase in genetic gain per year would be justification for stakeholders to invest more than $12 million per year to realize this gain.}, number={1}, journal={Journal of Forestry}, publisher={Oxford University Press (OUP)}, author={McKeand, Steven E and Payn, Kitt G and Heine, Austin J and Abt, Robert C}, year={2020}, month={Dec}, pages={62–72} }
 @article{heine_walker_mckeand_jett_isik_2020, title={Pollination Bag Type Has a Significant Impact on Cone Survival in Mass Production of Controlled Pollinated Seeds in Loblolly Pine}, volume={66}, ISSN={0015-749X 1938-3738}, url={http://dx.doi.org/10.1093/forsci/fxaa013}, DOI={10.1093/forsci/fxaa013}, abstractNote={Abstract
               Since 2009, deployment of full-sib families of loblolly pine (Pinus taeda L.) has gained prominence in the southeastern United States. To produce full-sib seed, a pollination bag is used to isolate female strobili from outside pollen contamination, and a known pollen is applied at the time of maximum female strobilus receptivity. The goal of this study was to compare prototype pollination bags made by PBS International to the industry standard kraft paper pollination bag with and without a support wire for female strobili survival and to assess their efficiency for mass production of controlled cross loblolly pine seed. A multiyear study compared 13 pollination bag types at more than nine seed orchard sites across the southeastern United States. There were significant differences among bag types for conelet survival at the time of bag removal that persisted until cone harvest 18 months later. Female strobili bagged in prototype PBS-I2 were over three times more likely to survive to cone harvest than strobili inside the traditional kraft pollination bag. Two of the PBS bag types had the highest estimated filled seed per bag. One PBS bag was faster to install and remove than the kraft paper bag with a support wire.}, number={5}, journal={Forest Science}, publisher={Oxford University Press (OUP)}, author={Heine, Austin J and Walker, Trevor D and McKeand, Steven E and Jett, Jackson B and Isik, Fikret}, year={2020}, month={Jun}, pages={589–599} }
 @phdthesis{comparison of pollination bags for mass production of controlled cross seeds in loblolly pine_2018, url={http://www.lib.ncsu.edu/resolver/1840.20/35063}, year={2018}, month={Apr} }